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D T J Littlewood - One of the best experts on this subject based on the ideXlab platform.
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on the position of archigetes and its bearing on the early evolution of the tapeworms
Journal of Parasitology, 2008Co-Authors: Peter D Olson, D T J Littlewood, L G Poddubnaya, Tomáš ScholzAbstract:The tapeworm Archigetes sieboldi Leuckart, 1878 (Platyhelminthes: Cestoda: Caryophyllidea) has been cited as a likely representative of the “protocestode” condition, owing to its lack of segmentation and ability to attain sexual maturity in the invertebrate host (aquatic oligochaetes). The idea has been variously amplified or rejected in the literature, although the actual phylogenetic position of the species has not been investigated until now. New collections of Archigetes sp. from both its vertebrate and invertebrate hosts provided the opportunity to estimate its phylogenetic position with the use of molecular systematics, while prompting new analyses aimed at assessing the early diversification of the Cestoda. Additional collections representing the Amphilinidea, Caryophyllidea, and Gyrocotylidea were combined with published gene sequences to construct data sets of complete 18S (110 taxa) and partial (D1-D3) 28S (107 taxa) rDNA sequences, including 8 Neodermatan outgroup taxa. Estimates resulting from...
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A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes)
BMC Evolutionary Biology, 2007Co-Authors: Joong-ki Park, Kyu-heon Kim, Seokha Kang, Won Kim, Keeseon S Eom, D T J LittlewoodAbstract:Background The parasitic Platyhelminthes (Neodermata) contains three parasitic groups of flatworms, each having a unique morphology, and life style: Monogenea (primarily ectoparasitic), Trematoda (endoparasitic flukes), and Cestoda (endoparasitic tapeworms). The evolutionary origin of complex life cyles (multiple obligate hosts, as found in Trematoda and Cestoda) and of endo-/ecto-parasitism in these groups is still under debate and these questions can be resolved, only if the phylogenetic position of the Monogenea within the Neodermata clade is correctly estimated. Results To test the interrelationships of the major parasitic flatworm groups, we estimated the phylogeny of the Neodermata using complete available mitochondrial genome sequences and a newly characterized sequence of a polyopisthocotylean monogenean Microcotyle sebastis . Comparisons of inferred amino acid sequences and gene arrangement patterns with other published flatworm mtDNAs indicate Monogenea are sister group to a clade of Trematoda+Cestoda. Conclusion Results confirm that vertebrates were the first host for stem group Neodermatans and that the addition of a second, invertebrate, host was a single event occurring in the Trematoda+Cestoda lineage. In other words, the move from direct life cycles with one host to complex life cycles with multiple hosts was a single evolutionary event. In association with the evolution of life cycle patterns, our result supports the hypothesis that the most recent common ancestor of the Neodermata giving rise to the Monogenea adopted vertebrate ectoparasitism as its initial life cycle pattern and that the intermediate hosts of the Trematoda (molluscs) and Cestoda (crustaceans) were subsequently added into the endoparasitic life cycles of the Trematoda+Cestoda clade after the common ancestor of these branched off from the monogenean lineage. Complex life cycles, involving one or more intermediate hosts, arose through the addition of intermediate hosts and not the addition of a vertebrate definitive host. Additional evidence is required from monopisthocotylean monogeneans in order to confirm the monophyly of the group.
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a common origin of complex life cycles in parasitic flatworms evidence from the complete mitochondrial genome of microcotyle sebastis monogenea platyhelminthes
BMC Evolutionary Biology, 2007Co-Authors: Joong-ki Park, Kyu-heon Kim, Seokha Kang, Won Kim, Keeseon S Eom, D T J LittlewoodAbstract:The parasitic Platyhelminthes (Neodermata) contains three parasitic groups of flatworms, each having a unique morphology, and life style: Monogenea (primarily ectoparasitic), Trematoda (endoparasitic flukes), and Cestoda (endoparasitic tapeworms). The evolutionary origin of complex life cyles (multiple obligate hosts, as found in Trematoda and Cestoda) and of endo-/ecto-parasitism in these groups is still under debate and these questions can be resolved, only if the phylogenetic position of the Monogenea within the Neodermata clade is correctly estimated. To test the interrelationships of the major parasitic flatworm groups, we estimated the phylogeny of the Neodermata using complete available mitochondrial genome sequences and a newly characterized sequence of a polyopisthocotylean monogenean Microcotyle sebastis. Comparisons of inferred amino acid sequences and gene arrangement patterns with other published flatworm mtDNAs indicate Monogenea are sister group to a clade of Trematoda+Cestoda. Results confirm that vertebrates were the first host for stem group Neodermatans and that the addition of a second, invertebrate, host was a single event occurring in the Trematoda+Cestoda lineage. In other words, the move from direct life cycles with one host to complex life cycles with multiple hosts was a single evolutionary event. In association with the evolution of life cycle patterns, our result supports the hypothesis that the most recent common ancestor of the Neodermata giving rise to the Monogenea adopted vertebrate ectoparasitism as its initial life cycle pattern and that the intermediate hosts of the Trematoda (molluscs) and Cestoda (crustaceans) were subsequently added into the endoparasitic life cycles of the Trematoda+Cestoda clade after the common ancestor of these branched off from the monogenean lineage. Complex life cycles, involving one or more intermediate hosts, arose through the addition of intermediate hosts and not the addition of a vertebrate definitive host. Additional evidence is required from monopisthocotylean monogeneans in order to confirm the monophyly of the group.
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the mitochondrial genome of gyrodactylus salaris platyhelminthes monogenea a pathogen of atlantic salmon salmo salar
Parasitology, 2006Co-Authors: Tine Huyse, Lutz Bachmann, Laetitia Plaisance, Bonnie L Webster, Tor A Bakke, D T J LittlewoodAbstract:In the present study, we describe the complete mitochondrial (mt) genome of the Atlantic salmon parasite Gyrodactylus salaris , the first for any monogenean species. The circular genome is 14 790 bp in size. All of the 35 genes recognized from other flatworm mitochondrial genomes were identified, and they are transcribed from the same strand. The protein-coding and ribosomal RNA (rRNA) genes share the same gene arrangement as those published previously for Neodermatan mt genomes (representing cestodes and digeneans only), and the genome has an overall A+T content of 65%. Three transfer RNA (tRNA) genes overlap with other genes, whereas the secondary structure of 3 tRNA genes lack the DHU arm and 1 tRNA gene lacks the TΨC arm. Eighteen regions of non-coding DNA ranging from 4 to 112 bp in length, totalling 278 bp, were identified as well as 2 large non-coding regions (799 bp and 768 bp) that were almost identical to each other. The completion of the mt genome offers the opportunity of defining new molecular markers for studying evolutionary relationships within and among gyrodactylid species.
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utility of complete large and small subunit rrna genes in resolving the phylogeny of the Neodermata platyhelminthes implications and a review of the cercomer theory
Biological Journal of The Linnean Society, 2003Co-Authors: Anne E Lockyer, Peter D Olson, D T J LittlewoodAbstract:We combined nearly complete sequences of large (LSU) and small (SSU) subunit rDNA from 32 flatworm species to estimate the phylogeny of the Platyhelminthes using maximum parsimony, maximum likelihood and Bayesian inference methods. Rooted against the Catenulida, combined evidence trees offered no support for the Revertospermata, which was also rejected by constraint analysis. Generally, nodal support was higher for groupings estimated from the combined data partitions and all methods of analysis provided congruent estimates of phylogeny. The Monogenea and Proseriata were resolved as monophyletic, rejecting previous suggestions of paraphyly based on SSU and partial LSU data sets and thus supporting widely accepted morphological synapomorphies. Monophyly of the Neodermata was supported and its sister group was a clade of neoophoran ‘turbellarians’ to the exclusion of the Proseriata which in turn was more basal. Taxa with similar spermatology to the Neodermata (Ichthyophaga, Notentera, Urastoma and Kronborgia) were the sister group to Tricladida + Prolecithophora, which in turn were sister to the Rhabdocoela. Polycladida + Macrostomida + Lecithoepitheliata was the earliest divergent offshoot of the Rhabditophora. Among the Neodermata, the Cercomeromorphae (Cestoda + Monogenea) was not supported, whereas Cestoda + Trematoda was well supported. Although there is no known synapomorphy for this latter grouping, our data highlight problems associated with the ‘cercomer theory’ and we reject putative homologies regarding Neodermatan ‘cercomers’ that have been sustained in the literature without careful scrutiny. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 78, 155–171.
Dong Zhang - One of the best experts on this subject based on the ideXlab platform.
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homoplasy or plesiomorphy reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata
International Journal for Parasitology, 2019Co-Authors: Dong Zhang, Wen X Li, Shan G Wu, Ming Li, Ivan Jakovlic, Jin Zhang, Rong Chen, Guitang WangAbstract:Abstract Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species (‘common GO’) within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest Neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of Neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.
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mitochondrial genomes of two thaparocleidus species platyhelminthes monogenea reveal the first rrna gene rearrangement among the Neodermata
International Journal of Molecular Sciences, 2019Co-Authors: Dong Zhang, Ivan Jakovlic, Jin Zhang, Rong Chen, Hong Zou, Gui T WangAbstract:Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.
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Additional file 5: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements
2018Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan JakovliÄ, Gui WangAbstract:Figure S2. The 23 unique gene orders in Neodermatan mitochondrial genomes filtered from 113 species. Representative species and corresponding taxonomic categories at the class/subclass level are shown on the left; a star symbol denotes that the gene order is shared by Monogenea and Cestoda. Pattern types used here to classify gene orders are shown on the right. In Lamellodiscus spari, the missing tRNAs are represented by the â?â symbol in the positions homologous to the closest available diplectanid relative, Lepidotrema longipenis. (PDF 1961 kb
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Additional file 6: Figure S3. of Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny
2017Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan Jakovlić, Gui WangAbstract:Gene orders of 107 Neodermatan mitochondrial genomes. Identical gene orders are indicated (and numbered) by a vertical black line on the right. To facilitate the comparison and distance calculation in CREx program, we have re-annotated the mt genomes for which trnS1 (AGN) , S2 (UCN) , L1 (CUN) and L2 (UUR) were ambiguously annotated with the help of ARWEN and MitoTool programs. Mt. genomes for which it was impossible to produce a reliable and consistent annotation were not used in the analysis. In detail: no tRNAs could be predicted by ARWEN for positions 11,564 to 11,635 in Orthocoelium streptocoelium NC_028071; 11,604 to 11,667 of Metorchis orientalis NC_028008; 11,606 to 11,665 of Fasciolopsis buski NC_030528; 11,717 to 11,785 of Fischoederius elongatus NC_028001; and 7304 to 7362 of Gastrothylax crumenifer NC_027833; rrnS was absent from Paragonimus westermani NC_002354, nad2 was absent from Fasciolopsis buski KX449331, nad3 was absent from Artyfechinostomum sufrartyfex KX943545; a duplicated trnS1 (AGN) was found in Metagonimus yokogawai NC_023249, and a duplicated trnC was found in Schistosoma mansoni NC_002545 and all the Schistosoma japonicum isolates. (PDF 4935 kb
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Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny
'Springer Science and Business Media LLC', 2017Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan Jakovlić, Gui T WangAbstract:Abstract Background Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes. Results The circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata. Conclusions This study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals
Gui T Wang - One of the best experts on this subject based on the ideXlab platform.
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mitochondrial genomes of two thaparocleidus species platyhelminthes monogenea reveal the first rrna gene rearrangement among the Neodermata
International Journal of Molecular Sciences, 2019Co-Authors: Dong Zhang, Ivan Jakovlic, Jin Zhang, Rong Chen, Hong Zou, Gui T WangAbstract:Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.
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Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny
'Springer Science and Business Media LLC', 2017Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan Jakovlić, Gui T WangAbstract:Abstract Background Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes. Results The circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata. Conclusions This study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals
Bernhard Egger - One of the best experts on this subject based on the ideXlab platform.
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Atp8 is in the ground pattern of flatworm mitochondrial genomes
BMC Genomics, 2017Co-Authors: Bernhard Egger, Lutz Bachmann, Bastian FrommAbstract:Background To date, mitochondrial genomes of more than one hundred flatworms (Platyhelminthes) have been sequenced. They show a high degree of similarity and a strong taxonomic bias towards parasitic lineages. The mitochondrial gene atp8 has not been confidently annotated in any flatworm sequenced to date. However, sampling of free-living flatworm lineages is incomplete. We addressed this by sequencing the mitochondrial genomes of the two small-bodied (about 1 mm in length) free-living flatworms Stenostomum sthenum and Macrostomum lignano as the first representatives of the earliest branching flatworm taxa Catenulida and Macrostomorpha respectively. Results We have used high-throughput DNA and RNA sequence data and PCR to establish the mitochondrial genome sequences and gene orders of S. sthenum and M. lignano . The mitochondrial genome of S. sthenum is 16,944 bp long and includes a 1,884 bp long inverted repeat region containing the complete sequences of nad3 , rrnS, and nine tRNA genes. The model flatworm M. lignano has the smallest known mitochondrial genome among free-living flatworms, with a length of 14,193 bp. The mitochondrial genome of M. lignano lacks duplicated genes, however, tandem repeats were detected in a non-coding region. Mitochondrial gene order is poorly conserved in flatworms, only a single pair of adjacent ribosomal or protein-coding genes – nad4l-nad4 – was found in S. sthenum and M. lignano that also occurs in other published flatworm mitochondrial genomes. Unexpectedly, we unambiguously identified the full metazoan mitochondrial protein-coding gene complement including atp8 in S. sthenum and M. lignano . A subsequent search detected atp8 in all mitochondrial genomes of polyclad flatworms published to date, although the gene wasn’t previously annotated in these species. Conclusions Manual, but not automated genome annotation revealed the presence of atp8 in basally branching free-living flatworms, signifying both the importance of manual data curation and of diverse taxon sampling. We conclude that the loss of atp8 within flatworms is restricted to the parasitic taxon Neodermata.
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A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms
Current biology : CB, 2015Co-Authors: Bernhard Egger, François Lapraz, Bartłomiej Tomiczek, Steven Müller, Christophe Dessimoz, Johannes Girstmair, Nives Škunca, Kate A. Rawlinson, Christopher B. Cameron, Elena BeliAbstract:The interrelationships of the flatworms (phylum Platyhelminthes) are poorly resolved despite decades of morphological and molecular phylogenetic studies [1, 2]. The earliest-branching clades (Catenulida, Macrostomorpha, and Polycladida) share spiral cleavage and entolecithal eggs with other lophotrochozoans. Lecithoepitheliata have primitive spiral cleavage but derived ectolecithal eggs. Other orders (Rhabdocoela, Proseriata, Tricladida and relatives, and Bothrioplanida) all have derived ectolecithal eggs but have uncertain affinities to one another. The orders of parasitic Neodermata emerge from an uncertain position from within these ectolecithal classes. To tackle these problems, we have sequenced transcriptomes from 18 flatworms and 5 other metazoan groups. The addition of published data produces an alignment of >107,000 amino acids with less than 28% missing data from 27 flatworm taxa in 11 orders covering all major clades. Our phylogenetic analyses show that Platyhelminthes consist of the two clades Catenulida and Rhabditophora. Within Rhabditophora, we show the earliest-emerging branch is Macrostomorpha, not Polycladida. We show Lecithoepitheliata are not members of Neoophora but are sister group of Polycladida, implying independent origins of the ectolecithal eggs found in Lecithoepitheliata and Neoophora. We resolve Rhabdocoela as the most basally branching euneoophoran taxon. Tricladida, Bothrioplanida, and Neodermata constitute a group that appears to have lost both spiral cleavage and centrosomes. We identify Bothrioplanida as the long-sought closest free-living sister group of the parasitic Neodermata. Among parasitic orders, we show that Cestoda are closer to Trematoda than to Monogenea, rejecting the concept of the Cercomeromorpha. Our results have important implications for understanding the evolution of this major phylum.
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Developmental diversity in free-living flatworms
EvoDevo, 2012Co-Authors: José María Martín-durán, Bernhard EggerAbstract:Flatworm embryology has attracted attention since the early beginnings of comparative evolutionary biology. Considered for a long time the most basal bilaterians, the Platyhelminthes (excluding Acoelomorpha) are now robustly placed within the Spiralia. Despite having lost their relevance to explain the transition from radially to bilaterally symmetrical animals, the study of flatworm embryology is still of great importance to understand the diversification of bilaterians and of developmental mechanisms. Flatworms are acoelomate organisms generally with a simple centralized nervous system, a blind gut, and lacking a circulatory organ, a skeleton and a respiratory system other than the epidermis. Regeneration and asexual reproduction, based on a totipotent neoblast stem cell system, are broadly present among different groups of flatworms. While some more basally branching groups - such as polyclad flatworms - retain the ancestral quartet spiral cleavage pattern, most flatworms have significantly diverged from this pattern and exhibit unique strategies to specify the common adult body plan. Most free-living flatworms (i.e. Platyhelminthes excluding the parasitic Neodermata) are directly developing, whereas in polyclads, also indirect developers with an intermediate free-living larval stage and subsequent metamorphosis are found. A comparative study of developmental diversity may help understanding major questions in evolutionary biology, such as the evolution of cleavage patterns, gastrulation and axial specification, the evolution of larval types, and the diversification and specialization of organ systems. In this review, we present a thorough overview of the embryonic development of the different groups of free-living (turbellarian) platyhelminths, including the Catenulida, Macrostomorpha, Polycladida, Lecithoepitheliata, Proseriata, Bothrioplanida, Rhabdocoela, Fecampiida, Prolecithophora and Tricladida, and discuss their main features under a consensus phylogeny of the phylum.
Rong Chen - One of the best experts on this subject based on the ideXlab platform.
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homoplasy or plesiomorphy reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata
International Journal for Parasitology, 2019Co-Authors: Dong Zhang, Wen X Li, Shan G Wu, Ming Li, Ivan Jakovlic, Jin Zhang, Rong Chen, Guitang WangAbstract:Abstract Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species (‘common GO’) within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest Neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of Neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.
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mitochondrial genomes of two thaparocleidus species platyhelminthes monogenea reveal the first rrna gene rearrangement among the Neodermata
International Journal of Molecular Sciences, 2019Co-Authors: Dong Zhang, Ivan Jakovlic, Jin Zhang, Rong Chen, Hong Zou, Gui T WangAbstract:Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.
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Additional file 5: of Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements
2018Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan JakovliÄ, Gui WangAbstract:Figure S2. The 23 unique gene orders in Neodermatan mitochondrial genomes filtered from 113 species. Representative species and corresponding taxonomic categories at the class/subclass level are shown on the left; a star symbol denotes that the gene order is shared by Monogenea and Cestoda. Pattern types used here to classify gene orders are shown on the right. In Lamellodiscus spari, the missing tRNAs are represented by the â?â symbol in the positions homologous to the closest available diplectanid relative, Lepidotrema longipenis. (PDF 1961 kb
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Additional file 6: Figure S3. of Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny
2017Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan Jakovlić, Gui WangAbstract:Gene orders of 107 Neodermatan mitochondrial genomes. Identical gene orders are indicated (and numbered) by a vertical black line on the right. To facilitate the comparison and distance calculation in CREx program, we have re-annotated the mt genomes for which trnS1 (AGN) , S2 (UCN) , L1 (CUN) and L2 (UUR) were ambiguously annotated with the help of ARWEN and MitoTool programs. Mt. genomes for which it was impossible to produce a reliable and consistent annotation were not used in the analysis. In detail: no tRNAs could be predicted by ARWEN for positions 11,564 to 11,635 in Orthocoelium streptocoelium NC_028071; 11,604 to 11,667 of Metorchis orientalis NC_028008; 11,606 to 11,665 of Fasciolopsis buski NC_030528; 11,717 to 11,785 of Fischoederius elongatus NC_028001; and 7304 to 7362 of Gastrothylax crumenifer NC_027833; rrnS was absent from Paragonimus westermani NC_002354, nad2 was absent from Fasciolopsis buski KX449331, nad3 was absent from Artyfechinostomum sufrartyfex KX943545; a duplicated trnS1 (AGN) was found in Metagonimus yokogawai NC_023249, and a duplicated trnC was found in Schistosoma mansoni NC_002545 and all the Schistosoma japonicum isolates. (PDF 4935 kb
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Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny
'Springer Science and Business Media LLC', 2017Co-Authors: Dong Zhang, Jin Zhang, Rong Chen, Hong Zou, Ivan Jakovlić, Gui T WangAbstract:Abstract Background Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes. Results The circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata. Conclusions This study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals
